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Background  Deer mice (genus  Peromyscus ) are the most common rodents in North America. Despite the availability of reference genomes for some species, a comprehensive database of polymorphisms, especially in those maintained as living stocks and distributed to academic investigators, is missing. In the present study we surveyed two populations of  P. maniculatus  that are maintained at the  Peromyscus  Genetic Stock Center (PGSC) for polymorphisms across their 2.5 × 10 9  bp genome.    Results  High density of variation was identified, corresponding to one SNP every 55 bp for the high altitude stock (SM2) or 207 bp for the low altitude stock (BW) using snpEff (v4.3). Indels were detected every 1157 bp for BW or 311 bp for SM2. The average Watterson estimator for the BW and SM2 populations is 248813.70388 and 869071.7671 respectively. Some differences in the distribution of missense, nonsense and silent mutations were identified between the stocks, as well as polymorphisms in genes associated with inflammation (NFATC2), hypoxia (HIF1a) and cholesterol metabolism (INSIG1) and may possess value in modeling pathology.    Conclusions  This genomic resource, in combination with the availability of  P. maniculatus  from the PGSC, is expected to promote genetic and genomic studies with this animal model.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-07956-w.

Genomic variation in captive deer mouse (Peromyscus maniculatus) populations